I'm making the transition from bowtie1 to bowtie2 and I was trying to replicate these results in bowtie1:
Now in bowtie2 I only get the best alignment, even though I'm using -a:
What am I doing wrong?
Code:
bowtie -a -v 2 --best e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT - gi|110640213|ref|NC_008253.1| 2852852 8:T>A - gi|110640213|ref|NC_008253.1| 148810 10:A>G,13:C>G + gi|110640213|ref|NC_008253.1| 1093035 2:T>G,15:A>T - gi|110640213|ref|NC_008253.1| 905664 6:A>G,7:G>T - gi|110640213|ref|NC_008253.1| 4930433 4:G>T,6:C>G
Code:
bowtie2 -x e_coli -a --end-to-end -c ATGCATCATGCGCCAT --no-hd 2> /dev/null | cut -f2-4,10,12- 16 gi|110640213|ref|NC_008253.1| 2852853 ATGGCGCATGATGCAT AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7T8 YT:Z:UU
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